Contacts of the strand formed by residues 143 - 152 (chain C) in PDB entry 4AEJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 143 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142C ARG* 1.3 79.7 - - - +
144C SER* 1.3 63.0 + - - +
211C ARG* 3.6 1.6 - - - +
212C THR 2.9 30.5 + - - +
215C ALA* 3.9 15.7 - - + +
218C LEU* 3.8 18.1 - - + +
242C VAL* 5.1 0.9 - - + -
243C CYS 3.1 13.5 - - - +
244C PHE* 3.7 24.7 - - + -
245C LEU 4.9 0.2 - - - +
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Residues in contact with SER 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C GLU* 4.0 13.3 + - - -
143C ALA* 1.3 76.9 - - - +
145C GLN* 1.3 63.5 + - - +
209C GLU* 4.9 2.2 + - - -
210C TYR 3.3 6.3 - - - -
211C ARG* 3.4 48.1 + - - -
218C LEU* 3.8 4.5 - - - -
242C VAL* 3.7 1.6 - - - +
243C CYS* 2.8 38.6 + - - +
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Residues in contact with GLN 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C TYR* 3.0 21.5 + - - -
144C SER* 1.3 77.4 - - - +
146C GLN* 1.3 71.2 - - - +
147C ILE 4.4 0.2 + - - -
209C GLU* 3.2 4.7 - - - -
210C TYR 3.0 32.2 + - - -
218C LEU* 4.0 7.3 - - + +
219C PRO* 3.6 10.1 - - - +
220C ILE* 2.8 54.3 - - + +
239C VAL* 3.3 8.7 - - - +
240C GLY 2.8 27.2 - - - +
241C PRO 3.4 9.9 - - - +
242C VAL* 4.0 8.7 - - + +
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Residues in contact with GLN 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C GLN* 1.3 81.2 - - - +
147C ILE* 1.3 64.3 + - - +
148C THR* 5.8 0.9 - - - +
192C LEU* 3.6 20.9 - - + +
207C VAL* 4.0 13.7 - - + +
208C PHE 3.0 9.4 - - - +
209C GLU* 3.1 37.2 + - + +
211C ARG* 5.0 1.4 - - - +
240C GLY* 3.1 28.1 + - - -
241C PRO 4.5 2.8 + - - -
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Residues in contact with ILE 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C PHE* 3.9 24.9 - - + -
146C GLN* 1.3 76.2 - - - +
148C THR* 1.3 63.5 + - - +
171C LEU* 3.6 45.1 - - + -
207C VAL* 4.7 0.9 - - - -
208C PHE* 2.9 47.7 + - + +
220C ILE* 4.0 13.5 - - + -
223C ILE* 4.1 8.5 - - + -
237C VAL* 3.5 28.3 - - + -
238C ASP 3.6 7.4 - - - +
239C VAL* 4.1 13.0 - - + -
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Residues in contact with THR 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C GLN* 5.8 0.9 - - - +
147C ILE* 1.3 72.1 + - - +
149C TYR* 1.3 61.7 + - - +
150C HIS* 3.8 14.8 + - + +
205C LYS* 3.8 39.0 + - + +
206C THR 3.5 7.4 - - - +
207C VAL* 3.8 18.0 - - + +
237C VAL* 3.2 10.4 - - - +
238C ASP* 2.8 52.3 + - - +
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Residues in contact with TYR 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ILE 3.9 1.4 + - - -
148C THR* 1.3 70.7 - - - +
150C HIS* 1.3 60.2 + - - +
151C CYS* 3.7 19.2 + - + -
154C SER* 2.7 30.0 + - - -
155C ILE 4.3 0.7 - - - -
156C ALA* 3.4 29.6 - - + -
169C LEU* 3.5 23.6 - - + -
196C CYS* 4.0 0.2 - - - -
205C LYS* 3.1 4.7 - - - -
206C THR 2.9 39.3 + - - +
208C PHE* 3.9 6.5 - - + -
223C ILE* 4.1 13.2 - - + -
225C PRO* 3.4 32.5 - - + +
228C ILE* 4.0 0.3 - - - +
235C PHE* 3.4 39.9 - + + +
236C GLY 3.7 7.9 - - - -
237C VAL* 4.6 2.0 - - + +
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Residues in contact with HIS 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C VAL 5.8 0.4 - - - -
91C ARG* 3.4 39.8 + - + +
148C THR* 4.0 17.7 - - + +
149C TYR* 1.3 71.6 - - - +
151C CYS* 1.3 59.3 + - - +
203C TRP* 3.8 3.8 - - + -
204C SER 3.4 4.6 + - - +
205C LYS* 3.8 19.3 - - + +
235C PHE* 3.0 12.1 - - - +
236C GLY* 2.8 50.7 + - - +
237C VAL 4.4 0.4 - - - -
238C ASP* 2.5 37.3 + - - -
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Residues in contact with CYS 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C TYR* 3.8 10.1 - - + -
150C HIS* 1.3 73.5 - - - +
152C LYS* 1.3 60.4 + - - +
153C ASN 5.8 0.4 - - - -
154C SER* 3.2 21.5 - - - +
196C CYS* 2.0 55.0 - - - -
202C GLU 3.5 1.6 - - - +
203C TRP* 3.4 8.1 - - - -
204C SER* 2.8 50.2 + - - -
234C GLU 3.9 3.1 - - - -
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Residues in contact with LYS 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C CYS* 1.3 75.0 - - - +
153C ASN* 1.3 75.5 - - - +
201C GLY 3.6 23.9 + - - +
202C GLU 3.8 13.9 - - - +
203C TRP* 3.7 37.8 - - + +
232C ASP* 3.7 18.6 - - - +
233C GLN* 3.5 1.0 - - - -
234C GLU* 3.0 57.7 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il